Merge pull request #4 from seek4science/gh-pages-1.16.0

1.16.0 update

_config.yml

@@ -1,7 +1,7 @@
 #baseurl: /seek
 
-current_seek_version: "1.15.2"
-current_docker_tag: "1.15"
+current_seek_version: "1.16.0"
+current_docker_tag: "1.16"
 
 plugins:
   - jekyll-sitemap

tech/earlier-upgrades.md

@@ -17,6 +17,106 @@ each released minor version in order incrementally (i.e. 0.13.x -> 0.14.x ->
 
 Each version has a tag, which has the format of *v* prefix
 followed by the version - e.g. v0.11.1, v0.13.2, v0.17.1
+
+## Steps to upgrade from 1.14.x to 1.15.x
+
+
+### Set RAILS_ENV
+
+**If upgrading a production instance of SEEK, remember to set the RAILS_ENV first**
+
+    export RAILS_ENV=production
+
+### Stopping services before upgrading
+
+    bundle exec rake seek:workers:stop 
+
+### Getting the upgrade
+
+The steps to fetch the upgrade will be different depending on whether it was originally installed directly
+from Github or via a downloaded tarball.
+
+#### Updating from GitHub
+
+If you have an existing installation linked to our GitHub, you can fetch the
+files with:
+
+    git fetch
+    git checkout v1.15.2
+
+#### Updating using the tarball
+
+You can download the file from
+<https://github.com/seek4science/seek/archive/v1.15.2.tar.gz> You can
+unpack this file using:
+
+    tar zxvf seek-1.15.2.tar.gz
+    mv seek seek-previous
+    mv seek-1.15.2 seek
+    cd seek/
+
+and then copy across your existing filestore and database configuration file
+from your previous installation and continue with the upgrade steps. The
+database configuration file you would need to copy is _config/database.yml_,
+and the filestore is simply _filestore/_
+
+### Install Python dependencies
+
+First, a specific version of `setuptools` needs to be installed to avoid an issue when installing dependencies
+
+    python3.9 -m pip install setuptools==58
+
+Then the other dependencies can be installed
+
+    python3.9 -m pip install -r requirements.txt
+
+### Upgrading Ruby
+
+It is necessary to upgrade to Ruby 3.1.4. If you are using [RVM](https://rvm.io/) (according to the [Installation Guide](install.html) )you should be prompted to install during the standard installation steps that follow.
+If you are not prompted you can install with the command:
+
+    rvm install $(cat .ruby-version)
+
+### Doing the upgrade
+
+After updating the files, the following steps will update the database, gems,
+and other necessary changes. Note that seek:upgrade may take longer than usual if you have data stored that points to remote
+content.
+
+**Please note** - during the upgrade the step _Updating session store_ can take a long time and appear that it has frozen, so please be patient.
+
+    cd . # this is to allow RVM to set the correct ruby version
+    gem install bundler
+    bundle install
+    bundle exec rake seek:upgrade
+    bundle exec rake assets:precompile # this task will take a while
+
+### Update Cron Services
+
+SEEK requires some cron jobs for periodic background jobs to run. To update these run:
+
+    bundle exec whenever --update-crontab
+
+### Restarting background job services
+
+    bundle exec rake seek:workers:start
+
+### Final notes
+
+If you encounter any problems with loading gems (likely _stringio_ or _strscan_) when running with Passenger, add the following to your Apache configuration:
+
+     PassengerPreloadBundler on
+
+more details at [PassengerPreloadBundler](https://www.phusionpassenger.com/docs/references/config_reference/apache/#passengerpreloadbundler)
+
+If using Nginx, the setting is
+
+     passenger_preload_bundler on;
+
+more details at [passenger_preload_bundler](https://www.phusionpassenger.com/docs/references/config_reference/nginx/#passenger_preload_bundler)
+
+---
+
 ## Steps to upgrade from 1.13.x to 1.14.x
 
 ### Dependencies

tech/extended-metadata/a-complete-example.md

@@ -0,0 +1,195 @@
+---
+title: A Complete Example to Create Extended Metadata Types by Uploading a JSON File
+layout: page
+---
+
+<a href="create-extended-metadata-type-with-json-file.html">back</a>
+
+# A Complete Example
+
+
+## Step 1: Define Controlled Vocabularies 
+
+Currently, controlled vocabularies can only be created through the user interface by anyone with permission to create resources in SEEK
+
+You can also use the following direct link  ```HTTP://{HOST_NAME}/sample_controlled_vocabs/new``` to create controlled vocabularies or the button on the [Controlled Vocabulary](manage-extended-metadata-type.html/#3-controlled-vocabularies-tab) tab.
+
+Assuming the controlled vocabularies have been created here:
+<img src="/images/user-guide/extended-metadata/cvs-tab.png" alt="extended-metadata-fields" width="600">
+
+You can view the detailed controlled vocabularies by clicking the corresponding its ID. 
+<img src="/images/user-guide/extended-metadata/role_name_identifier_scheme_cv.png" alt="extended-metadata-fields" width="500">
+
+## Step 2: Define Nested Exended Metadata Types
+
+1. Define a metadata type named `role_name_identifiers` with two attributes: `scheme` and `identifier`. After creation, it is assigned ID `158`.
+
+```json
+{
+  "title": "role_name_identifiers",
+  "supported_type": "ExtendedMetadata",
+  "enabled": true,
+  "attributes": [
+    {
+      "title": "scheme",
+      "type": "Controlled Vocabulary",
+      "required": true,
+      "ID": 14, // ID of CV "Role Name Identifier Scheme"
+      "label": "scheme",
+      "description": "scheme"
+    },
+    {
+      "title": "identifier",
+      "type": "String",
+      "required": false,
+      "label": "identifier",
+      "description": "identifier"
+    }
+  ]
+}
+```
+
+2.Define a new metadata type called `role_emt`, which will have one attribute linked to the previously created `role_name_identifiers`. Consequently, the `role_emt` type will be established with five attributes and assigned the ID 159.
+
+```json
+{
+  "title": "role_emt",
+  "supported_type": "ExtendedMetadata",
+  "enabled": true,
+  "attributes": [
+    {
+      "title": "role_name_personal_title",
+      "type": "Controlled Vocabulary",
+      "required": true,
+      "ID": 13, // ID of CV "Role Name Personal Title"
+      "label": "personal title",
+      "description": "personal title"
+    },
+    {
+      "title": "first_name",
+      "type": "String",
+      "required": false,
+      "label": "first name",
+      "description": "first name"
+    },
+    {
+      "title": "last_name",
+      "type": "String",
+      "required": false,
+      "label": "last name",
+      "description": "last name"
+    },
+    {
+      "title": "role_type",
+      "type": "Controlled Vocabulary",
+      "required": true,
+      "ID": 12, // ID of CV "Role type"
+      "label": "role type",
+      "description": "role type"
+    },
+    {
+      "title": "role_name_identifiers",
+      "type": "Linked Extended Metadata (multiple)",
+      "required": false,
+      "ID": 158, // ID of the nested metadata type `role_name_identifiers`
+      "label": "role name identifiers",
+      "description": "role name identifiers"
+    }
+  ]
+}
+```
+
+
+
+## Step 3: Define Top Level Extended Metadata Type for Study
+
+```json
+{
+  "title": "An example with all attribute types",
+  "supported_type": "Study",
+  "enabled": true,
+  "attributes": [
+    {
+      "title": "title",
+      "required": true,
+      "type": "String",
+      "label": "study title",
+      "description": "study title"
+    },
+    {
+      "title": "description",
+      "required": true,
+      "type": "Text",
+      "label": "study description",
+      "description": "study description"
+    },
+    {
+      "title": "study_start_date",
+      "required": true,
+      "type": "Date",
+      "label": "study start date",
+      "description": "study start date"
+
+    },
+    {
+      "title": "study_start_time",
+      "required": true,
+      "type": "Date time",
+      "label": "study start time",
+      "description": "study start time"
+    },
+    {
+      "title": "study_age",
+      "required": true,
+      "type": "Integer",
+      "label": "study age",
+      "description": "study age"
+    },
+    {
+      "title": "cholesterol_level",
+      "required": true,
+      "type": "Real number",
+      "label": "cholesterol level",
+      "description": "cholesterol level"
+    },
+    {
+      "title": "resource_use_rights_authors_confirmation",
+      "required": true,
+      "type": "Boolean",
+      "label": "resource use rights authors confirmation",
+      "description": "resource use rights authors confirmation"
+    },
+    {
+      "title": "resource_type_general",
+      "required": true,
+      "type": "Controlled Vocabulary",
+      "ID": 16, // ID of CV "resource_type_general"
+      "label": "resource type general",
+      "description": "resource type general"
+    },
+    {
+      "title": "resource_study_country",
+      "type": "Controlled Vocabulary List",
+      "required": true,
+      "ID": 15, // ID of CV "European Study Country"
+      "label": "study country",
+      "description": "study country"
+    },
+    {
+      "title": "role",
+      "type": "Linked Extended Metadata (multiple)",
+      "required": false,
+      "ID": 159, // ID of the nested metadata type `role_emt`
+      "label": "role",
+      "description":"role"
+    }
+  ]
+}
+```
+
+## Step 4: Use Extended Metadata Type 
+
+As the result, you can choose to load this extended metadata type on the study creation page.
+![](/images/user-guide/extended-metadata/emt-ui.png)
+
+